Open Science Workflow Cheatsheet

Key terms

• Repository: A place to store code, files, and each file’s revision history.
  
• Local Computer: Your physical computer.
  
• Remote: Computer that is located elsewhere and accessed over a network (e.g. the internet).
  
• Render: Generate documents, presentations and more. Produce HTML, PDF, MS Word, reveal.js, MS Powerpoint, Beamer, websites, blogs, books…

Git and GitHub

Starting a repository

flowchart TD
    A(Do you have a directory already started on your local computer?  ) --Yes--> B(git init)
    A --No  --> C(git clone repository_url)

git init: Initialize a Git repository on a local computer.
git clone repository_url: Copying an entire repository onto a local computer.

Making changes to repository

git status: Check what files have changed.
git restore filename: Undo changes to a file.

flowchart LR
    A(Local computer) --> B(Stage changes: git add)
    B --> C(Commit changes: git commit -m)
    C --> D(Push changes to remote repository: git push)
    D --> E(Remote repository)

flowchart LR 
    A(Remote repository) --> B(Pull changes from remote: git pull)
    B --> C(Local computer)

From your local computer

git add: Stage changes for a local commit.
git commit -m "short, descriptive message": Commit changes to be tracked.
git push: Push changes from local computer up to the remote repository.

From remote repository

git pull: Pull changes from the remote repository to your local computer.
git pull origin main: Pull changes from the remote repository main branch to the branch you are on.

Branches

git checkout -b branch_name: Create a new branch.
git checkout branch_name: Switch to a different branch.
git switch: Switch to a different branch.

VSCode

An IDE (integrated development environment) that works well with many languages.

Side Bar Options

File Explorer

To browse the files in a project

Git GUI (Source Control)

To interact with your GitHub repository

Extensions

VS Code’s version of the app store

R

Similar to the options available in RStudio for viewing variables in your environment, function documentation, and installing packages.

Command Palette

Use the shortcut ctl + shift + P to access.

Terminal

Can have multiple terminals of different languages running at a time.

renv

Initialize renv for a project

renv::init(): Set up a project library for a new or existing project.

Install new packages

renv::install(): Install packages from CRAN, GitHub, etc..

Lockfile

renv::snapshot(): Update the lockfile with packages being used.
renv::restore(): Reinstall the packages specified in the lockfile.

Shiny

ui.R: the interactive user interface code (to show stuff)
server.R: the code for computations and plotting (to do stuff)
shiny::shinyApp(): launches the app

Quarto

Document format

In the header yaml, specify what format(s) you want to create.

---
title: "Open Science Workflow Cheatsheet"
format: html
---

format options include:

• html
  
• pdf
  
• revealjs
  
• docx
  
• and more!

Including code

Include code blocks in a document

```{r}
#| echo: true

x <- 2+2
```

Calculated values can be reported in text later: \(x =\) 4.

And control the output rendered in the document with execution options.

Option	Effects
echo	show/hide code in output
eval	do/don’t run code
include	include/exclude code or results
output	include/exclude results
warning	show/hide warnings in output
error	show/hide error in output and continue with render

To render document

To render a quarto file to the proper format, in your terminal (not R), run:

quarto render path/to/file/name.qmd